Hi all,
I am looking for a tool or software package that can help me infer the evolution of gene content within a given phylogeny. Is anybody aware of such a thing?
In more detail, let's assume that I have a phylogeny and a vector of gene copy numbers (0 for gene absence, 1 for single copy, 2 for a duplicated gene and so on) per external node of the phylogeny. This represents the gene content for a gene X in extant taxa. I am looking for a tool that can infer events such as gene gain, loss, duplication (and possibly HGT) across the phylogeny, either using maximum parsimony or (preferably) a probabilistic approach. If the latter approach is used, I'd also like the estimates for the rate of such events.
If anyone known of an existing tool or can point me in the right direction, that would be very helpful!
Thanks.